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During the battle of Damocles, Jeremiah Gottwald fights Anya Alstreim, and after damaging the Mordred, he is about to kill her. However, from what I remember, he doesn't; instead we see him about to activate his Geass Canceler.

Now by this point in time, we already know that Anya was afflicted with Geass by Marianne when V.V. killed her, and Marianne's power allowed her consciousness to reside in Anya. Before Ragnarok begins, Anya is taken over by Marianne before leaving with C.C. to a Twilight Gate to reach the Sword of Akasha. At this point, she leaves Anya's body, and later dies when Lelouch uses his Geass on God.

This would mean the Geass Affliction Anya had is now dispelled. So what was it that Jeremiah saw in Anya which prompted him to use the Geass Canceler on her?

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It was not officially said but it was implied that Charles had actually been using his Geass on Anya for years to erase her memories. If you remember Jeremiah activated his Geass Canceler right after Anya revealed that she had no memories. Presumably, the memory erasing was to prevent her from discovering Marianne's presence or some similar event. Throughout the series Charles is the only one was is able to erase or delete memories and he is also in a key position to be erasing them and he would want to keep Marianne existence hidden.

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